RetrogeneDB ID:

retro_dord_185

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:GeneScaffold_4850:1068828..1069242(+)
Located in intron of:ENSDORG00000014622
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rps18
Ensembl ID:ENSDORG00000013825
Aliases:None
Description:ribosomal protein S18 [Source:MGI Symbol;Acc:MGI:98146]


Retrocopy-Parental alignment summary:






>retro_dord_185
ATGTCTTTAGTGATTCCTGAGAAGTTCCAGCACATTTTGTGAGTACTCAACACCAATATCGATGGGCGGTGGAAAATAGC
CTTTGCCAGCACTGCCATTAAGGGTGTGGGGCGAAGATCCGCTCACGTAGTGTTGAGGAAGGCGGACGCTGACGTCACCA
AGAGGGCTGGAGTACTCACAGAGGATGAGGGGGAACGTGTGATTACCGCTATGCAGAATCCAAGTCAGTACAAGATCCCA
GACTGGTTCTTAAACACACAGAAGGATGGAAAGGATGGAAAATGCAGCCAGGTTCTGGCCCATGGTCTAGATAATAAGCT
CCATGAAGACCTGGAGCAGCTTAAAAAGATTCGAGCCCATGGAGGGCTGCGCCACTTCTGGGGCCTTCGAGTCAGAGGCC
AACACACCAAGACC

ORF - retro_dord_185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.33 %
Parental protein coverage: 90.79 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLVIPEKFQHILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITI
MSLVIPEKFQHIL.VLNTNIDGR.KIAFA.TAIKGVGRR.AHVVLRKAD.D.TKRAG.LTEDE.ERVIT.
RetrocopyMSLVIPEKFQHIL*VLNTNIDGRWKIAFASTAIKGVGRRSAHVVLRKADADVTKRAGVLTEDEGERVITA
ParentalMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKT
MQNP.QYKIPDWFLN.Q........SQVLA.GLDNKL.EDLE.LKKIRAH.GLRHFWGLRVRGQHTKT
RetrocopyMQNPSQYKIPDWFLNTQXXXXXXXCSQVLAHGLDNKLHEDLEQLKKIRAHGGLRHFWGLRVRGQHTKT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Dipodomys ordii was not studied using RNA-Seq expression data.
Dipodomys ordii was not studied using ChIP-Seq data.
Dipodomys ordii was not studied using EST data.
Dipodomys ordii was not studied using FANTOM5 data.
retro_dord_185 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 14 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009507 retrocopies
Dipodomys ordii ENSDORG00000013825 6 retrocopies
Gorilla gorilla ENSGGOG000000065715 retrocopies
Loxodonta africana ENSLAFG000000321731 retrocopy
Macaca mulatta ENSMMUG000000038671 retrocopy
Mus musculus ENSMUSG000000086682 retrocopies
Nomascus leucogenys ENSNLEG0000000684010 retrocopies
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
Procavia capensis ENSPCAG000000058542 retrocopies
Pongo abelii ENSPPYG0000002595314 retrocopies
Pan troglodytes ENSPTRG000000180391 retrocopy
Rattus norvegicus ENSRNOG000000285054 retrocopies
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
Sarcophilus harrisii ENSSHAG000000086581 retrocopy



Copyright © RetrogeneDB 2014-2017